Diversification of the Caenorhabditis heat shock response by Helitron transposable elements
- University of California, San Diego, United States
Figures
Figure 1 with 1 supplement
Helitrons contribute a significant number of HSEs to the C. elegans genome.
(A) Number of Helitrons that overlap with 101 bp regions centered around HSF-1 peak summits (ChIP-seq data from Li et al. (2016); peaks called using MACS2, Zhang et al., 2008) in non-heat shock …
Figure 1—figure supplement 1
Genome-wide distributions of Hin- and Hac-HSEs.
Numbers of Hin- (gray) and Hac-HSEs (red) within 1 kb bins along the length of each C. elegans chromosome. The approximate positions of full-length (FL) Helitron1_CE elements are shown using blue …
Figure 2 with 1 supplement
HSR genes with adjacent Hac- or Hin-HSEs display different properties.
(A) Heatmap displaying normalized (see Materials and methods for details) HSF-1 and Pol II ChIP-seq reads over 2 kb regions centered on Hac-HSE- and Hin-HSE-containing HS HSF-1 peak summits. ChIP …
Figure 2—figure supplement 1
HSR genes with adjacent Hac- or Hin-HSEs display different levels of histone modifications associated with gene expression or repression.
(A) Notched boxplot showing distributions of H3K9me3 ChIP-seq reads using publicly available data obtained from L3 stage worms during NHS conditions (Ho et al., 2014) over Hac- or Hin-HSE HSR gene …
Figure 3
Helitrons contribute significant numbers of HSEs to other Caenorhabditis genomes.
(A) Phylogeny of all metazoan genomes hosted at the UCSC genome browser (genome.ucsc.edu) that have RepeatMasker-generated annotations of repetitive elements (see Supplementary file 5 for genome …
Figure 4
Hac-HSEs are associated with distinct gene sets up-regulated by HS in C. elegans and C. briggsae.
(A) Number of C. elegans HS UP genes (n = 1462) within 500 bp bins vs. distance from Hac- and Hin-HSEs. HS UP genes are defined as those with a fold change after HS >2 and an adjusted p-value<0.01 …
Figure 5
Hac-HSEs diversify the HSR in C. elegans.
(A) Genome browser screenshot depicting the region surrounding the Hac-HSE HSR gene nhr-247 showing normalized ChIP-seq signal for HSF-1 and Pol II under NHS and HS conditions (ChIP-seq data …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Genetic reagent (C. elegans) | N2 | wild-type strain | ||
| Genetic reagent (C. elegans) | QX1211 | Wild isolate | ||
| Genetic reagent (C. elegans) | MY16 | Wild isolate | ||
| Genetic reagent (C. briggsae) | AF16 | wild-type strain | ||
| Commercial assay or kit | Illumina TruSeq Stranded Total RNA Library Prep Gold Kit | Illumina | Illumina: 20020598 | |
| Software, algorithm | FigTree v1.4.4 | http://tree.bio.ed.ac.uk/software/figtree/ | ||
| Software, algorithm | Bowtie2 v2.3.3.1 | Langmead and Salzberg, 2012 | Sequence alignment | |
| Software, algorithm | MEME v5.0.3 | Bailey and Elkan, 1994 | Motif finder | |
| Software, algorithm | Tomtom v5.0.2 | Gupta et al., 2007 | Motif comparison | |
| Software, algorithm | Cistrome | Liu et al., 2011 | Generation of heat maps | |
| Software, algorithm | DESeq2 v1.18.1 | Love et al., 2014 | Differential expression analysis of RNA-seq | |
| Software, algorithm | Delly v0.8.1 | Rausch et al., 2012 | Genome comparisons | |
| Software, algorithm | bcftools v1.9 | Narasimhan et al., 2016 | Genome comparisons |
Additional files
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Supplementary file 1
Transcription Factor motifs in Helitrons.
Enrichment of Transcription Factor motifs found within C. elegans Helitrons compared to genome-wide occurences.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp1-v2.xlsx
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Supplementary file 2
Heat shock-induced gene expression of L2 stage N2 C. elegans.
RNA-seq results showing fold change in gene expression of C. elegans subjected to heat shock at 34°C versus control animals at 20°C for 30 min.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp2-v2.xlsx
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Supplementary file 3
C. elegans Hin-HSE genes up-regulated by heat shock.
List of HSR genes containing Helitron independent HSEs (Hin-HSEs) bound by HSF-1.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp3-v2.xlsx
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Supplementary file 4
C. elegans Hac-HSE genes up-regulated by heat shock.
List of HSR genes containing Helitron acquired HSEs (Hac-HSEs) bound by HSF-1.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp4-v2.xlsx
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Supplementary file 5
Presence of HSEs in Helitrons across species.
Analysis of HSEs located within annotated Helitrons for species available at the UCSC Genome Browser.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp5-v2.xlsx
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Supplementary file 6
Presence of HSEs in Helitrons in Caenorhabditis genomes.
Analysis of HSEs located within annotated Helitrons for species available through the Caenorhabditis Genome Project.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp6-v2.xlsx
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Supplementary file 7
Heat shock-induced gene expression of L2 stage AF16 C. briggsae.
RNA-seq results showing fold change in gene expression of C. briggsae subjected to heat shock at 34°C versus control animals at 20°C for 30 min.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp7-v2.xlsx
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Supplementary file 8
Comparison of Hin-HSE and Hac-HSE genes up-regulated by heat shock in C. elegans and C. briggsae.
List of HSR genes containing Helitron independent HSEs (Hin-HSEs) and Helitron acquired (Hac-HSEs) in C. elegans and C. briggsae.
- https://cdn.elifesciences.org/articles/51139/elife-51139-supp8-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/51139/elife-51139-transrepform-v2.pdf
